3LQF
Crystal structure of the short-chain dehydrogenase Galactitol-Dehydrogenase (GatDH) of Rhodobacter sphaeroides in complex with NAD and erythritol
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.7 | 291 | 100MM MES, 200MM MAGNESIUMCHLORIDE, 14.0%(W/V)MPEG5000, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 41.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.863 | α = 90 |
b = 113.838 | β = 90 |
c = 123.234 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RAYONIX | MIRRORS | 2008-10-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | BESSY | 14.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||
1 | 1.8 | 30 | 99.9 | 0.078 | 0.078 | 17.65 | 7.3 | 83822 | 83822 | 28.474 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.8 | 1.85 | 99.3 | 0.68 | 0.68 | 2.96 | 6.8 | 6087 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | SWISS PROT MODEL | 1.8 | 30 | 79631 | 79631 | 4191 | 100 | 0.1861 | 0.1861 | 0.18419 | 0.22267 | RANDOM | 24.924 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.49 | 2.36 | -1.87 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.583 |
r_dihedral_angle_4_deg | 17.487 |
r_dihedral_angle_3_deg | 15.112 |
r_dihedral_angle_1_deg | 5.96 |
r_scangle_it | 3.24 |
r_scbond_it | 2.062 |
r_angle_refined_deg | 1.389 |
r_mcangle_it | 1.331 |
r_mcbond_it | 0.787 |
r_chiral_restr | 0.093 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7392 |
Nucleic Acid Atoms | |
Solvent Atoms | 509 |
Heterogen Atoms | 210 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |